Effects of oxaliplatin on DNA condensation

In this paper the interactions between DNA and anti-cancer drug oxaliplatin were investigated by using magnetic tweezers. The dynamics of DNA condensation due to oxaliplatin was traced under various forces. It is found that torsion constraint in DNA enhances the ability of oxaliplatin for shortening DNA. The transplatin helps oxaliplatin combine to DNA and increase the rate of DNA condensation. All these results are consistent to the previously proposed model and are helpful for further investigation of interaction between DNA and oxaliplatin.     

Morphology evolution of Si nanowires synthesized by gas condensation of SiO without any catalyst

A series of Si nanowires are synthesized at constant temperature of 970 ^○C on Si substrate by gas condensation of pure SiO vapor without any metal catalysts, by controlling the coverage of SiO_x deposits. The morphologies are characterized by scan electron microscopy (SEM) and their evolution during the growth process is observed: from isolated clusters in earlier stage to linked cluster assemblies, and developing to smooth nanowires in the later stage. The growth mechanism is discussed based on the newly proposed clustering-aggregation-sintering model.     

珠状凝结换热的数学物理模型及数值模拟

首次应用随机分形模型建立了珠状凝结液滴的空间和尺度分布,然后利用已有的单个液滴的传热规律,得到了冷凝壁面的换热边界条件,进而求解冷凝壁的温度分布,最后得到了平均的珠状凝结换热系数.应用上述模型对铜表面以水为介质的冷凝壁换热进行了直接数值模拟,并与各种压力条件下的试验数据进行了比较.     

Denaturation transition of stretched DNA

We generalize the Poland-Scheraga model to consider DNA denaturation in the presence of an external stretching force. We demonstrate the existence of a force-induced DNA denaturation transition and obtain the temperature-force phase diagram. The transition is determined by the loop exponent c, for which we find the new value c = 4 nu-1/2 such that the transition is second order with c = 1.85 < 2 in d = 3. We show that a finite stretching force F destabilizes DNA, corresponding to a lower melting temperature T(F), in agreement with single-molecule DNA stretching experiments.     

Structural polymorphism of DNA-dendrimer complexes

DNA condensation in vivo relies on electrostatic complexation with small cations or large histones. We report a synchrotron x-ray study of the phase behavior of DNA complexed with synthetic cationic dendrimers of intermediate size and charge. We encounter unexpected structural transitions between columnar mesophases with in-plane square and hexagonal symmetries, as well as liquidlike disorder. The isoelectric point is a locus of structural instability. A simple model is proposed based on competing long-range electrostatic interactions and short-range entropic adhesion by counterion release.     

High-resolution vibrational spectroscopy of the OH− ion in an Mg-related defect in LiF and NaF

Summary High-resolution (0.05 cm⁻¹) FTIR spectroscopy in the range (9÷300) K is applied to study the vibrational (stretching, bending and combination) modes of OH⁻ (and its isotopic substitution with OD⁻) perturbed by a neighbouring defect induced by Mg²⁺ in LiF and NaF. The stretching-mode spectra are analysed in the framework of the anharmonic-oscillator model: the related Morse parameters have been determined. A model is proposed for the defect, responsible for the stretching line and two bending lines, which are accounted for by an inversion doubling. In honour of Prof. Fausto Fumi on the occasion of his retirement from teaching.     

Acceleration of silanol condensation of a methacryl-functional silane in the model sizing system

The silanol condensation of hydrolyzed γ-methacryloxypropyltrimethoxysilane (γ-MPS) in the presence of a typical film-forming polymer, poly(vinyl acetate), PVAc, has been studied. The model sizing system, consisting of the hydrolyzates of γ-MPS and PVAc obtained from the alcoholic aqueous solution, is studied using Fourier transform infrared spectroscopy (FT-IR) and size exclusion chromatography (SEC). In the initial stage of silanol condensation of the hydrolyzates of the model sizing system, it has been found that the condensation reaction is accelerated compared with the system that contains no film-former. It has also been found that the structure of γ-MPS oligomer is relatively ordered and less-active for further silanol condensation. The least-square curve-fitting procedure for FT-IR spectra indicates five carbonyl stretching bands, reflecting the hydrogen bonded and the free carbonyl groups of the silane coupling agent and the film-forming polymer.     

Effect of Torsion on Cisplatin-Induced DNA Condensation

We investigate the effect of torsion on DNA condensation with the covalently closed circular DNA as the torsionconstrained system, using an atomic force microscope. It is found that there are two stages in the DNA condensation process under torsional constraint. At the early stage, the low torsion will accelerate DNA condensation by promoting the formation of micro-loops or intersection structures; while at the later stage, the increasing torsion will slow it down by preventing the crosslinking of cisplatin and DNA since the DNA molecule becomes more rigid. Our results show the important role of torsion in DNA condensation and sheds new light on the mechanism for DNA condensation.     

Effect of Laser Field and Mechanical Force on Deoxyribonucleic Acid Melting

We propose a physics method to study the effect of laser field and mechanical force on the melting process of double-stranded deoxyribonucleic acid （DNA）. A two-dimensional lattice model is established for DNA molecules stuck on the surface, and the stretching energy of the hydrogen bond and stacking energy for each DNA molecule are calculated by using a nonlinear potential. A real-time algorithm is employed to deal with the dynamics process of DNA melting. Numerical results explain the experimental observations. The spatial distribution of the laser field determines the sequences of DNA melting. The simulation has shown the dependence of the final number of melted DNA on the laser field and mechanical force.     

Strain softening in stretched DNA

The microscopic mechanics of DNA stretching was characterized using extensive molecular dynamics simulations. By employing an anisotropic pressure-control method, realistic force-extension dependences of effectively infinite DNA molecules were obtained. A coexistence of B and S DNA domains was observed during the overstretching transition. The simulations revealed that strain softening may occur in the process of stretching torsionally constrained DNA. The latter observation was qualitatively reconciled with available experimental data using a random-field Ising model.     

基于变温紫外分光光度法研究温度对DNA凝聚过程影响

荧光单分子实验结果表明温度能够促进DNA凝聚,随着温度升高,精胺(亚精胺)-DNA凝聚体系中DNA凝聚构象趋于更加紧致、有序。为探究温度对不同高价离子-DNA凝聚体系的影响,利用自行搭建的变温紫外分光光度计,通过系统研究荧光单分子实验中采用的精胺(亚精胺)-DNA凝聚体系及去离子水中DNA在260 nm处特征吸收值随温度变化情况,确定了DNA凝聚构象与其260 nm处特征吸收值之间的对应关系为：DNA凝聚构象越紧致、有序,其对应的260 nm处紫外吸收值越低。在此基础上,系统地研究了DNA凝聚实验中常用四种钴胺化合物-DNA凝聚体系随温度变化情况,结果表明三氯六胺合钴与精胺(亚精胺)类似,其对应的DNA凝聚体系在260 nm特征吸收值,随着温度升高而逐渐降低,即DNA凝聚构象趋于更加紧致、有序。而三(乙二胺)氯化钴、反式双(乙二胺)氯化钴、五胺氯化钴的情况却不同,与其对应的DNA凝聚体系在260 nm特征吸收值,随着温度升高,呈现先增加,再降低,然后再增加的规律。     

Mass-spectrometric study of tellurium-film condensation and evaporation on sapphire

The processes of the condensation and evaporation of a tellurium film produced by a molecular beam of Te₂ on a sapphire surface are studied. It is experimentally shown that the desorption of tellurium from a surface upon growth under nonequilibrium conditions exceeds the equilibrium thermal desorption. If the beam intensity is less than the equilibrium value, then desorption is also lower than the equilibrium value. A model of this process with allowance for the transient states of tellurium in the adsorption layer is proposed. Within this model equilibrium and Langmuir beams are expressed in terms of the process parameters. The reflection coefficient of the beam is also a function of the process characteristics. The experimental data make it possible to estimate some of the basic parameters of the process, including the coverage and desorption rate in the adsorption layer. Taking these results into account is important for manufacturing perfect films not only of Te, but also of CdTe.     

Connection of Gibbs layer gatherings with rate of mass transfer upon deposition of thin films with presence of impurity

The Gibbs layer gatherings on the condensation front of silver vapor in the presence of water vapor are analyzed. The front of condensation for analyzing the Gibbs concentration excess is calculated with the use of the modified Langmuir’s model of sorption. At a fixed flow of silver vapor and temperature of the substrate, the water-vapor pressure varies. Calculations have shown that the change of the water-vapor pressure changes the structure of the silver condensate, the structure of Gibbs layers, and microroughness on the condensation front. As a consequence, the efficiency of mass transfer varies. With growth of the water-vapor pressure, the condensation efficiency of both vapor components decreases. For obtaining the most equal surface of condensed silver film there is an optimum water-vapor pressure. The results allow the influence of noncondensed gas impurity on growth of thin films to be understood in greater detail and help to choose optimum modes for vacuum deposition. A general conclusion regarding the connection of the Gibbs layers and microroughness of the condensation surface with the intensity of mass transfer, leaving a framework of vacuum deposition processes, is drawn.     

Effect of electroelastic anisotropy of DNA-like molecules on their tertiary structure

Under certain conditions, mechanical forces can cause an anisotropic molecule like DNA to assume a toroidal spatial structure. A simple model describing such a behavior is suggested. The model incorporates anisotropic elastic energy and external electrical forces. The steady-state structures formed by a macromolecule have been studied numerically using this model. There exist ranges of model parameters, namely, the anisotropy of the elastic tensor, magnitude and orientation of forces, and modulation periods, where molecules have toroidal, spherical, or extended structures. Estimates of parameters characteristic of these structures are consistent with experimental data. In particular, the toroidal structure dimension corresponds to experimental dimensions of toroidal globules produced as a result of so-called PSI condensation of DNA molecules. Zh. éksp. Teor. Fiz. 112, 2156–2168 (December 1997)     

AMP和DNA的银溶胶增强拉曼光谱

本文报道了生物分子5‘-腺苷磷酸（AMP）和脱氧核糖核酸（DNA）在银溶胶中的增强拉曼光谱。实验结果表明用银溶胶增加方法可以得到在较低浓度下、几乎不受光干扰的增强拉曼光谱。与固体AMP和DNA拉曼光谱进行比较,发现谱峰有很好的一致性,但也存在差异,如对应于固体AMP中715cm^-1处的腺嘌呤的呼吸振动峰加强,并位移到723cm^-1处,813cm^-1处的磷酸酯的对称伸缩振动峰消失了;在DNA中核糖环的振动峰明显加强,A,T,C,G四种碱基的峰也得到了不同程度的增强。通过对实验结果的分析,推测了AMP和DNA在银溶胶界面的吸附状态和分子结构。     

Effects of Ionic Dependence of DNA Persistence Length on the DNA Condensation at Room Temperature

DNA persistence length is a key parameter for quantitative interpretation of the conformational properties of DNA and related to the bending rigidity of DNA.A series of experiments pointed out that,in the DNA condensation process by multivalent cations,the condensed DNA takes elongated coil or compact globule states and the population of the compact globule states increases with an increase in ionic concentration.At the same time,single molecule experiments carried out in solution with multivalent cations(such as spermidine,spermine)indicated that DNA persistence length strongly depends on the ionic concentration.In order to revolve the effects of ionic concentration dependence of persistence length on DNA condensation,a model including the ionic concentration dependence of persistence length and strong correlation of multivalent cation on DNA is provided.The autocorrelation function of the tangent vectors is found as an effective way to detect the ionic concentration dependence of toroidal conformations.With an increase in ion concentration,the first periodic oscillation contained in the autocorrelation function shifts,the number of segment contained in the first periodic oscillation decreases gradually.According to the experiments,the average long-axis length is defined to estimate the ionic concentration dependence of condensation process further.The relation between long-axis length and ionic concentration matches the experimental results qualitatively.     

Laser-induced fluorescence spectrum of argon matrix-isolated dichlorocarbene

Dichlorocarbene has been prepared for spectral investigation by the matrix reaction of alkali metal atoms with carbon tetrachloride at high dilution in argon followed by condensation onto a copper wedge held at 15 K. When these samples were irradiated with laser lines of wavelengths between 5682 and 4545 Å, an intense red emission system peaking around 7000 Å was observed. The spectrum of this emission revealed at least five progressions in the ground state bending and stretching fundamentals. A revised value of the ground state bending mode for CCl₂ was obtained from higher-resolution spectra using more diluted samples and various laser exciting frequencies. Carbon-13 enriched samples confirm the assignments of the bands to progressions in the ground state bending and symmetric stretching modes of CCl₂.     

低压蒸汽滴状冷凝过程中液滴生长特性

研究了低压条件对滴状冷凝过程液滴生长特性的影响。首先,研究了超疏水表面上空气环境和蒸汽环境中附着液滴的接触角,发现蒸汽环境中的接触角比空气环境中的小,而蒸汽压力对接触角没有显著影响。第二,实验研究了冷凝过程中的液滴的生长周期和脱落尺寸,液滴的脱落半径随压力的降低而增大,生长周期也随之延长。第三,实验研究了液滴合并生长速率,并结合理论分析直接冷凝长大的生长速率,直接冷凝生长速率随压力的减小而减小,并随过冷度的减小而下降,而实验范围内合并生长速率不受压力影响。第四,根据滴状冷凝液滴分布的时间序列模型,分析了不同压力下液滴生长的临界尺寸,随着压力的降低,液滴生长方式的临界尺寸增大。     

OctTES/TEOS system for hybrid coatings: real‐time monitoring of the hydrolysis and condensation by Raman spectroscopy

The hybrid organic–inorganic system Tetra‐ethyl‐ortho‐silicate functionalized with Octyl‐triethoxy‐silane, studied as protective coating for the preservation of historical glasses from the environmental weathering agents, has been characterized by Raman spectroscopy by monitoring the sol‐gel reactions over time through characteristic features in the spectrum. In particular, for the hydrolysis reaction the disappearance of the 653 cm⁻¹ (Si‐O symmetric breathing) and 810 cm⁻¹ (CH₂ rocking in Si‐alkoxides) peaks and the growth of the 710 cm⁻¹ band, because of hydrolyzed alkyl‐silane, and of the 881 cm⁻¹ peak (ethanol C–C symmetric stretching) have been checked. Moreover, the condensation reaction can be tracked by the disappearance of the two main peaks of the alcohols at 816 and 881 cm⁻¹, going along with the growth of the broad band between 250 and 500 cm⁻¹ (Si–O–Si symmetric bending) and of the feature at 840 cm⁻¹ (Si–O–Si stretching). At the end of the condensation process the Raman spectrum still displays spectral bands unique to the alkyl chain in Octyl‐triethoxy‐silane, in the 1330–1450 cm⁻¹ and 2725–3000 cm⁻¹ ranges. Copyright © 2016 John Wiley & Sons, Ltd.     

Particle size prediction of magnesium nanoparticle produced by inert gas condensation method

Properties of nanoparticles are normally depending on particle size; therefore, developing a model to predict particle size is of vital importance. This paper established an energy analysis model to predict average particle size of magnesium nanoparticles fabricated by inert gas condensation method. Predictions of average particle size ranging from 20 to 50 nm by energy analysis model have relative errors of less than 10% compared with experimental research. Further, the model is applied to investigate operation conditions to decrease the average particle size of magnesium nanoparticles. It is found that decreasing the absolute pressure in the condensation room and increasing the temperature rise of the inert gas can both produce nanoparticles with smaller average particle sizes. Temperature rise of the inert gas plays a more important role in effect on average nanoparticle size than the absolute pressure in the condensation room. Energy transformed by collision bonding and dissipated by convection are the dominant processes for particle growth when number of atoms in one particle is greater than 2000 atoms.